Besides the different colors the only other difference was the base tune loaded in the EEC.
K&N FIPK, Steeda, JLT. Those three seem to be the most popular and they all produce results within a couple HP/TQ of each other. I think the JLT is the leat expensive of the three and the K&N is the only "C.A.R.B. Certified" CAI.
I asked a similar question. I noted the the tunes on the 04 and 03 cobras lent them selves to different pickups when using an SCT tunner. If you go too there website the 04 picks up a lot of HP and the 03 picks up a lot of tourque...LOL
It's like they switched the tunes for more torque factory stock in the 04's over HP like the 03's. I could be backwards on that but I think thats I had found out about the tunes.